Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
Bioinformatics Program, Loyola University Chicagogrid.164971.c, Chicago, Illinois, USA.
Microbiol Spectr. 2021 Dec 22;9(3):e0094221. doi: 10.1128/spectrum.00942-21.
The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota.
尿路的微生物群落（尿路微生物群或尿路微生物组）与人类健康有关。细菌的全基因组测序是一种强大的工具，允许研究尿路微生物组（尿微生物组）的基因组内容。细菌质粒是尿路微生物组的重要组成部分，但研究不足。由于质粒可以作为临床相关特征的载体和储库，因此它们对尿路微生物组的动态具有重要意义，因此可能与尿路健康有关。在这个项目中，我们在 11 种临床相关的尿路物种中寻找质粒：尿球菌、棒状杆菌、粪肠球菌、大肠杆菌、阴道加德纳菌、肺炎克雷伯菌、格氏乳杆菌、詹氏乳杆菌、表皮葡萄球菌、咽峡炎链球菌和缓症链球菌。我们在粪肠球菌、大肠杆菌、肺炎克雷伯菌、表皮葡萄球菌和咽峡炎链球菌中发现了质粒的证据，但在迄今为止测序的其他物种中证据不足。一些鉴定的质粒组装被预测具有潜在的毒力和/或抗生素耐药基因，尽管它们注释的编码区大部分功能未知。在这项研究中，我们报告了尿路物种中的质粒，作为了解质粒在细菌尿路微生物组中作用的第一步。尿路的微生物群落（尿路微生物群）与人类健康有关。细菌的全基因组测序允许检查尿路微生物群的基因组，包括质粒。由于质粒是临床相关特征的载体和储库，因此它们对尿路微生物群的动态具有重要意义，因此可能与尿路健康有关。目前，尿路微生物群中的质粒研究不足。在这里，我们在 11 种临床相关的尿路物种中寻找质粒。我们在粪肠球菌、大肠杆菌、肺炎克雷伯菌、表皮葡萄球菌和咽峡炎链球菌中发现了质粒的证据，但在其他 6 种物种中证据不足。我们在一些质粒组装中鉴定出潜在的毒力和/或抗生素耐药基因，但它们注释的编码区大部分功能未知。这是了解质粒在细菌尿路微生物组中作用的第一步。
